From 1cb0fc264a1899a34c1439f48d2ddc6c9ba826bb Mon Sep 17 00:00:00 2001
From: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
Date: Wed, 30 Oct 2024 10:24:20 -0700
Subject: [PATCH] Simplify development installation (#198)

* add all optional dependencies to dev requirements

* update contributing guide

* update PR test action
---
 .github/workflows/pr.yml | 2 +-
 CONTRIBUTING.md          | 4 ++--
 pyproject.toml           | 3 +--
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
index 02b20b08..19a0409a 100644
--- a/.github/workflows/pr.yml
+++ b/.github/workflows/pr.yml
@@ -33,6 +33,6 @@ jobs:
           python -m pip install --upgrade pip
           # Install cpu wheels only to speed up the build
           pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
-          pip install ".[metrics,dev]"
+          pip install ".[dev]"
       - name: Test with pytest
         run: pytest -v
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 44db5bbc..51602c83 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -3,11 +3,11 @@
 ## Development installation
 
 Clone or fork the repository,
-then make an editable installation with all the optional dependencies:
+then make an editable installation with all the development dependencies:
 
 ```sh
 # in project root directory (parent folder of pyproject.toml)
-pip install -e ".[dev,visual,metrics]"
+pip install -e ".[dev]"
 ```
 
 ## CI requirements
diff --git a/pyproject.toml b/pyproject.toml
index 99e9a737..55be6805 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,7 +41,6 @@ metrics = [
     "captum>=0.7.0",
 ]
 examples = ["napari", "jupyter", "jupytext"]
-
 visual = [
     "ipykernel",
     "graphviz",
@@ -51,8 +50,8 @@ visual = [
     "nbformat",
     "cmap",
 ]
-
 dev = [
+    "viscy[metrics,examples,visual]",
     "pytest",
     "pytest-cov",
     "hypothesis",